Contacts of the strand formed by residues 202 - 206 (chain B) in PDB entry 4PBY
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 202 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 4.0 24.9 - - + -
195B SER 3.1 15.7 - - - +
196B ALA* 4.9 1.6 - - - -
201B THR* 1.3 79.1 - - - +
203B CYS* 1.3 61.0 + - - +
222B ILE* 3.3 5.2 - - - +
223B PHE* 2.8 44.5 + - + +
226B HIS* 4.3 9.0 - - + -
230B VAL* 4.1 15.3 - - + -
233B VAL* 4.0 14.8 - - + -
243B PHE* 4.2 8.1 - - + -
245B SER* 3.5 33.7 - - - +
255B TRP* 3.8 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B GLY* 3.6 31.9 - - - -
176B HIS* 3.5 28.0 - - - +
193B LEU 3.7 0.9 - - - +
194B LEU* 3.4 8.1 - - - +
195B SER* 3.0 31.8 + - - -
201B THR* 4.5 2.7 - - - -
202B ILE* 1.3 72.8 - - - +
204B LEU* 1.3 59.5 + - - +
205B TRP* 3.5 25.9 - - + -
219B ALA* 4.1 4.9 - - + -
221B THR 3.6 3.8 - - - -
222B ILE* 3.9 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B HIS* 4.3 11.9 - - + +
193B LEU 3.4 13.2 - - - +
194B LEU* 3.9 11.2 - - + -
202B ILE 4.3 0.2 + - - -
203B CYS* 1.3 73.4 - - - +
205B TRP* 1.3 78.7 - - - +
219B ALA* 3.4 5.5 - - - -
220B LYS* 2.9 42.3 + - + -
221B THR* 2.9 32.6 + - - +
223B PHE* 4.1 9.4 - - + -
235B TRP* 3.7 27.1 - - + -
257B THR* 4.4 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B VAL* 3.8 28.3 - - + -
173B LEU* 3.3 42.6 - - + +
174B ARG 2.8 32.7 + - - -
175B GLY 4.3 0.4 - - - -
176B HIS* 4.0 8.3 - + - -
191B GLY 3.3 1.6 - - - +
192B HIS* 3.3 3.8 - - - -
193B LEU* 2.7 53.0 + - + +
195B SER* 3.5 24.2 - - - -
203B CYS* 3.5 23.8 - - + -
204B LEU* 1.3 78.2 - - - +
206B ASP* 1.3 59.2 + - - +
207B ILE* 4.4 8.5 - - + -
217B VAL* 3.4 20.0 + - + -
218B ASP 3.4 8.1 - - - -
219B ALA* 3.0 26.2 - - + +
220B LYS 4.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLY 3.6 3.4 - - - -
192B HIS* 2.7 38.4 + - + +
204B LEU* 5.0 0.4 - - + +
205B TRP* 1.3 71.2 - - - +
207B ILE* 1.3 59.2 + - - +
208B SER* 2.4 50.0 + - - -
209B ALA* 3.7 4.0 + - - -
210B VAL* 4.3 6.9 - - - +
217B VAL* 4.6 6.7 - - - +
220B LYS* 4.5 24.2 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il